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Abstract

In this chapter we review proteomic studies performed on purified postsynaptic density (PSD) fractions and analyze what their results reveal about nuclear signaling. Overall, these studies show that PSDs are similar to the cytoplasmic protein complexes found at other intercellular junctions. We find that PSDs contain numerous calmodulin (CAM)-associated transcriptional coactivators, nucleocytoplasmic shuttling proteins that bind RNA and potential splicing factors. Moreover, in conjunction with bioinformatics, we identify novel nucleocytoplasmic shuttling proteins at synapses. These results strongly suggest that control of the spatial distribution of synapse-associated nuclear factors regulates nuclear function.

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References

  • Aplin, A. E., and Juliano, R. L. (2001) Regulation of nucleocytoplasmic trafficking by cell adhesion receptors and the cytoskeleton. J. Cell Biol. 155, 187–191.

    PubMed  CAS  Google Scholar 

  • Ataman, B., Ashley, J., Gorczyca, D., Gorczyca, M., Mathew, D., Wichmann, C., Sigrist, S. J., and Budnik, V. (2006) Nuclear trafficking of Drosophila Frizzled-2 during synapse development requires the PDZ protein dGRIP. Proc. Natl. Acad. Sci. USA 103, 7841–7846.

    Google Scholar 

  • Balda, M. S., and Matter, K. (2000) The tight junction protein ZO-1 and an interacting tran scription factor regulate ErbB-2 expression. EMBO J. 19, 2024–2033.

    PubMed  CAS  Google Scholar 

  • Banker, G., Churchill, L., and Cotman, C. W. (1974) Proteins of the postsynaptic density. J. Cell Biol. 63, 456–465.

    PubMed  CAS  Google Scholar 

  • Beesley, P. W., Mummery, R., and Tibaldi, J. (1995) N-cadherin is a major glycoprotein component of isolated rat forebrain postsynaptic densities. J. Neurochem. 64, 2288–2294.

    PubMed  CAS  Google Scholar 

  • Beffert, U., Weeber, E. J., Durudas, A., Qiu, S., Masiulis, I., Sweatt, J. D., Li, W. P., Adel mann, G., Frotscher, M., Hammer, R. E., and Herz, J. (2005) Modulation of synaptic plasticity and memory by Reelin involves differential splicing of the lipoprotein receptor ApoEr2. Neuron 47, 567–579.

    PubMed  CAS  Google Scholar 

  • Bianchi, E., Denti, S., Granata, A., Bossi, G., Geginat, J., Villa, A., Rogge, L., and Pardi, R. (2000) Integrin LFA-1 interacts with the transcriptional co-activator JAB1 to modulate AP-1 activity. Nature 404, 617–621.

    PubMed  CAS  Google Scholar 

  • Black, D. L., and Graveley, B. R. (2006) Splicing bioinformatics to biology. Genome Biol. 7, 317.

    PubMed  Google Scholar 

  • Blaustein, M., Pelisch, F., Tanos, T., Munoz, M. J., Wengier, D., Quadrana, L., Sanford, J. R., Muschietti, J. P., Kornblihtt, A. R., Caceres, J. F., et al. (2005) Concerted regulation of nuclear and cytoplasmic activities of SR proteins by AKT. Nat. Struct. Mol. Biol. 12, 1037–1044.

    PubMed  CAS  Google Scholar 

  • Butz, S., and Kemler, R. (1994) Distinct cadherin-catenin complexes in Ca(2+)-dependent cell-cell adhesion. FEBS Lett. 355, 195–200.

    PubMed  CAS  Google Scholar 

  • Cao, X., and Sudhof, T. C. (2001) A transcriptionally active complex of APP with Fe65 and histone acetyltransferase Tip60. Science 293, 115–120.

    PubMed  CAS  Google Scholar 

  • Carlin, R. K., Grab, D. J., Cohen, R. S., and Siekevitz, P. (1980) Isolation and characteriza tion of postsynaptic densities from various brain regions: enrichment of different types of postsynaptic densities. J. Cell Biol. 86, 831–845.

    PubMed  CAS  Google Scholar 

  • Chakraborty, S., Reineke, E. L., Lam, M., Li, X., Liu, Y., Gao, C., Khurana, S., and Kao, H. Y. (2006)α-Actinin 4 Potentiates Myocyte Enhancer Factor-2 Transcription Activ ity by Antagonizing Histone Deacetylase 7. J. Biol. Chem. 281, 35070–35080.

    PubMed  CAS  Google Scholar 

  • Chan, C. S., Weeber, E. J., Kurup, S., Sweatt, J. D., and Davis, R. L. (2003) Integrin require ment for hippocampal synaptic plasticity and spatial memory. J. Neurosci. 23, 7107–7116.

    PubMed  CAS  Google Scholar 

  • Chawla, S., Vanhoutte, P., Arnold, F. J., Huang, C. L., and Bading, H. (2003) Neuronal activ ity-dependent nucleocytoplasmic shuttling of HDAC4 and HDAC5. J. Neurochem. 85, 151–159.

    PubMed  CAS  Google Scholar 

  • Chen, J. T., Lu, D. H., Chia, C. P., Ruan, D. Y., Sabapathy, K., and Xiao, Z. C. (2005) Im paired long-term potentiation in c-Jun N-terminal kinase 2-deficient mice. J. Neurochem. 93, 463–473.

    PubMed  CAS  Google Scholar 

  • Chih, B., Gollan, L., and Scheiffele, P. (2006) Alternative splicing controls selective trans- synaptic interactions of the neuroligin-neurexin complex. Neuron 51, 171–178.

    PubMed  CAS  Google Scholar 

  • Chung, H. J., Xia, J., Scannevin, R. H., Zhang, X., and Huganir, R. L. (2000) Phosphorylation of the AMPA receptor subunit GluR2 differentially regulates its interaction with PDZ domain-containing proteins. J. Neurosci. 20, 7258–7267.

    PubMed  CAS  Google Scholar 

  • Cioce, M., and Lamond, A. I. (2005) CAJAL BODIES: A Long History of Discovery. Annu. Rev. Cell Dev. Biol. 21, 105–131.

    PubMed  CAS  Google Scholar 

  • Cohen, R. S., Blomberg, F., Berzins, K., and Siekevitz, P. (1977) The structure of postsynap tic densities isolated from dog cerebral cortex. I. Overall morphology and protein com position. J. Cell Biol. 74, 181–203.

    CAS  Google Scholar 

  • Collins, M. O., Husi, H., Yu, L., Brandon, J. M., Anderson, C. N., Blackstock, W. P., Choudhary, J. S., and Grant, S. G. (2006) Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome. J. Neurochem. 97 Suppl 1, 16–23.

    Google Scholar 

  • Consortium, I. H. G. S. (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931–945.

    Google Scholar 

  • Cyert, M. S. (2001) Regulation of nuclear localization during signaling. J. Biol. Chem. 276, 20805–20808.

    PubMed  CAS  Google Scholar 

  • D’Arcangelo, G., Miao, G. G., Chen, S. C., Soares, H. D., Morgan, J. I., and Curran, T. (1995) A rotein related to extracellular matrix proteins deleted in the mouse mutant reeler. Nature 374, 719–723.

    PubMed  CAS  Google Scholar 

  • Deisseroth, K., Mermelstein, P. G., Xia, H., and Tsien, R. W. (2003) Signaling from synapse to nucleus: the logic behind the mechanisms. Curr. Opin. Neurobiol. 13, 354–365.

    PubMed  CAS  Google Scholar 

  • Dosemeci, A., Tao-Cheng, J. H., Vinade, L., and Jaffe, H. (2006) Preparation of postsynaptic density fraction from hippocampal slices and proteomic analysis. Biochem. Biophys. Res. Commun. 339, 687–694.

    PubMed  CAS  Google Scholar 

  • Dye, B. T., and Patton, J. G. (2001) An RNA recognition motif (RRM) is required for the localization of PTB-associated splicing factor (PSF) to subnuclear speckles. Exp. Cell Res. 263, 131–144.

    PubMed  CAS  Google Scholar 

  • Fagotto, F., Funayama, N., Gluck, U., and Gumbiner, B. M. (1996) Binding to cadherins antagonizes the signaling activity of beta-catenin during axis formation in Xenopus. J. Cell Biol. 132, 1105–1114.

    PubMed  CAS  Google Scholar 

  • Feng, Y., Gutekunst, C. A., Eberhart, D. E., Yi, H., Warren, S. T., and Hersch, S. M. (1997) Fragile X mental retardation protein: nucleocytoplasmic shuttling and association with somatodendritic ribosomes. J. Neurosci. 17, 1539–1547.

    PubMed  CAS  Google Scholar 

  • Flavell, S. W., Cowan, C. W., Kim, T. K., Greer, P. L., Lin, Y., Paradis, S., Griffith, E. C., Hu, L. S., Chen, C., and Greenberg, M. E. (2006) Activity-dependent regulation of MEF2 transcription factors suppresses excitatory synapse number. Science 311, 1008–1012.

    PubMed  CAS  Google Scholar 

  • Fu, X., McGrath, S., Pasillas, M., Nakazawa, S., and Kamps, M. P. (1999) EB-1, a tyrosine kinase signal transduction gene, is transcriptionally activated in the t(1;19) subset of pre-B ALL, which express oncoprotein E2a-Pbx1. Oncogene 18, 4920–4929.

    PubMed  CAS  Google Scholar 

  • Fujii, R., Okabe, S., Urushido, T., Inoue, K., Yoshimura, A., Tachibana, T., Nishikawa, T., Hicks, G. G., and Takumi, T. (2005) The RNA binding protein TLS is translocated to dendritic spines by mGluR5 activation and regulates spine morphology. Curr. Biol. 15, 587–593.

    PubMed  CAS  Google Scholar 

  • Fujii, R., and Takumi, T. (2005) TLS facilitates transport of mRNA encoding an actin-stabilizing protein to dendritic spines. J. Cell Sci. 118, 5755–5765.

    PubMed  CAS  Google Scholar 

  • Gall, J. G. (2003) The centennial of the Cajal body. Nat. Rev. Mol. Cell Biol. 4, 975–980.

    PubMed  CAS  Google Scholar 

  • Gama-Carvalho, M., Carvalho, M. P., Kehlenbach, A., Valcarcel, J., and Carmo-Fonseca, M. (2001) Nucleocytoplasmic shuttling of heterodimeric splicing factor U2AF. J. Biol. Chem. 276, 13104–13112.

    PubMed  CAS  Google Scholar 

  • Gattoni, R., Mahe, D., Mahl, P., Fischer, N., Mattei, M. G., Stevenin, J., and Fuchs, J. P. (1996) The human hnRNP-M proteins: structure and relation with early heat shock- induced splicing arrest and chromosome mapping. Nucleic Acids Res. 24, 2535–2542.

    PubMed  CAS  Google Scholar 

  • Gerrow, K., and El-Husseini, A. (2006) Cell adhesion molecules at the synapse. Front. Biosci. 11, 2400–2419.

    PubMed  CAS  Google Scholar 

  • Ghersi, E., Noviello, C., and D’Adamio, L. (2004) Amyloid-beta protein precursor (AbetaPP) intracellular domain-associated protein-1 proteins bind to AbetaPP and modulate its processing in an isoform-specific manner. J. Biol. Chem. 279, 49105–49112.

    PubMed  CAS  Google Scholar 

  • Gordon, M. D., and Nusse, R. (2006) Wnt signaling: multiple pathways, multiple receptors, and multiple transcription factors. J. Biol. Chem. 281, 22429–22433.

    PubMed  CAS  Google Scholar 

  • Gorlich, D., and Kutay, U. (1999) Transport between the cell nucleus and the cytoplasm. Annu. Rev. Cell Dev. Biol. 15, 607–660.

    PubMed  CAS  Google Scholar 

  • Gottardi, C. J., Arpin, M., Fanning, A. S., and Louvard, D. (1996) The junction-associated protein, zonula occludens-1, localizes to the nucleus before the maturation and during the remodeling of cell-cell contacts. Proc. Natl. Acad. Sci. USA 93, 10779–10784.

    PubMed  CAS  Google Scholar 

  • Graef, I. A., Mermelstein, P. G., Stankunas, K., Neilson, J. R., Deisseroth, K., Tsien, R. W., and Crabtree, G. R. (1999) L-type calcium channels and GSK-3 regulate the activity of NF-ATc4 in hippocampal neurons. Nature 401, 703–708.

    PubMed  CAS  Google Scholar 

  • Guzowski, J. F., Lyford, G. L., Stevenson, G. D., Houston, F. P., McGaugh, J. L., Worley, P. F., and Barnes, C. A. (2000) Inhibition of activity-dependent arc protein expression in the rat hippocampus impairs the maintenance of long-term potentiation and the consolidation of long-term memory. J. Neurosci. 20, 3993–4001.

    PubMed  CAS  Google Scholar 

  • Hallier, M., Lerga, A., Barnache, S., Tavitian, A., and Moreau-Gachelin, F. (1998) The transcription factor Spi-1/PU.1 interacts with the potential splicing factor TLS. J. Biol. Chem. 273, 4838–4842.

    PubMed  CAS  Google Scholar 

  • Hardingham, G. E., Arnold, F. J., and Bading, H. (2001) Nuclear calcium signaling controls CREB-mediated gene expression triggered by synaptic activity. Nat. Neurosci. 4, 261–267.

    PubMed  CAS  Google Scholar 

  • Hatzfeld, M. (2005) The p120 family of cell adhesion molecules. Eur J. Cell Biol. 84, 205–214.

    PubMed  CAS  Google Scholar 

  • Havik, B., Rokke, H., Bardsen, K., Davanger, S., and Bramham, C. R. (2003) Bursts of high- frequency stimulation trigger rapid delivery of pre-existing alpha-CaMKII mRNA to synapses: a mechanism in dendritic protein synthesis during long-term potentiation in adult awake rats. Eur J. Neurosci. 17, 2679–2689.

    PubMed  Google Scholar 

  • Honda, K., Yamada, T., Endo, R., Ino, Y., Gotoh, M., Tsuda, H., Yamada, Y., Chiba, H., and Hirohashi, S. (1998) Actinin-4, a novel actin-bundling protein associated with cell motility and cancer invasion. J. Cell Biol. 140, 1383–1393.

    PubMed  CAS  Google Scholar 

  • Hsueh, Y. P., and Sheng, M. (1999) Regulated expression and subcellular localization of syndecan heparan sulfate proteoglycans and the syndecan-binding protein CASK/LIN-2 during rat brain development. J. Neurosci. 19, 7415–7425.

    PubMed  CAS  Google Scholar 

  • Hsueh, Y. P., Wang, T. F., Yang, F. C., and Sheng, M. (2000) Nuclear translocation and tran scription regulation by the membrane-associated guanylate kinase CASK/LIN-2. Nature 404, 298–302.

    PubMed  CAS  Google Scholar 

  • Huber, K. M., Gallagher, S. M., Warren, S. T., and Bear, M. F. (2002) Altered synaptic plas ticity in a mouse model of fragile X mental retardation. Proc. Natl. Acad. Sci. USA 99, 7746–7750.

    PubMed  CAS  Google Scholar 

  • Huber, O., Korn, R., McLaughlin, J., Ohsugi, M., Herrmann, B. G., and Kemler, R. (1996) Nuclear localization of beta-catenin by interaction with transcription factor LEF-1. Mech. Dev. 59, 3–10.

    PubMed  CAS  Google Scholar 

  • Hubner, S., Jans, D. A., and Drenckhahn, D. (2001) Roles of cytoskeletal and junctional plaque proteins in nuclear signaling. Int. Rev. Cytol. 208, 207–265.

    PubMed  CAS  Google Scholar 

  • Hulsken, J., Birchmeier, W., and Behrens, J. (1994) E-cadherin and APC compete for the interaction with beta-catenin and the cytoskeleton. J. Cell Biol. 127, 2061–2069.

    PubMed  CAS  Google Scholar 

  • Husi, H., Ward, M. A., Choudhary, J. S., Blackstock, W. P., and Grant, S. G. (2000) Proteo mic analysis of NMDA receptor-adhesion protein signaling complexes. Nat. Neurosci. 3, 661–669.

    PubMed  CAS  Google Scholar 

  • Hyson, R. L., and Rubel, E. W. (1995) Activity-dependent regulation of a ribosomal RNA epitope in the chick cochlear nucleus. Brain Res. 672, 196–204.

    PubMed  CAS  Google Scholar 

  • Irwin, S. A., Patel, B., Idupulapati, M., Harris, J. B., Crisostomo, R. A., Larsen, B. P., Kooy, F., Willems, P. J., Cras, P., Kozlowski, P. B., et al. (2001) Abnormal dendritic spine characteristics in the temporal and visual cortices of patients with fragile-X syndrome: a quantitative examination. Am. J. Med. Genet. 98, 161–167.

    PubMed  CAS  Google Scholar 

  • Jones, R. B., Gordus, A., Krall, J. A., and MacBeath, G. (2006) A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439, 168–174.

    PubMed  CAS  Google Scholar 

  • Jordan, B. A., Fernholz, B. D., Boussac, M., Xu, C., Grigorean, G., Ziff, E. B., and Neubert, T. A. (2004) Identification and verification of novel rodent postsynaptic density proteins. Mol. Cell Proteomics. 3, 857–871.

    PubMed  CAS  Google Scholar 

  • Jordan, B. A., Fernholz, B. D., Neubert, T. A., and Ziff, E. B. (2006) The Dynamic Synapse: Molecular Methods in Ionotropic Receptor Biology. CRC/Taylor & Francis, Boc Raton.

    Google Scholar 

  • Jordan, B. A., Fernholz, B. D., Khatri, L., Ziff, E. B. (2007) Activity-dependent AIDA-1 nuclear signaling regulates nucleolar numbers and protein synthesis in neurons. Nat. Neurosci. 10, 427–35.

    PubMed  CAS  Google Scholar 

  • Kaltschmidt, C., Kaltschmidt, B., and Baeuerle, P. A. (1995) Stimulation of ionotropic gluta mate receptors activates transcription factor NF-kappa B in primary neurons. Proc. Natl. Acad. Sci. USA 92, 9618–9622.

    PubMed  CAS  Google Scholar 

  • Kameoka, S., Duque, P., and Konarska, M. M. (2004) p54(nrb) associates with the 5’ splice site within large transcription/splicing complexes. EMBO J. 23, 1782–1791.

    PubMed  CAS  Google Scholar 

  • Kandel, E. R. (2001) The molecular biology of memory storage: a dialogue between genes and synapses. Science 294, 1030–1038.

    PubMed  CAS  Google Scholar 

  • Kaul, S. C., Kawai, R., Nomura, H., Mitsui, Y., Reddel, R. R., and Wadhwa, R. (1999) Identi fication of a 55-kDa ezrin-related protein that induces cytoskeletal changes and localizes to the nucleolus. Exp. Cell Res. 250, 51–61.

    PubMed  CAS  Google Scholar 

  • Kausalya, P. J., Phua, D. C., and Hunziker, W. (2004) Association of ARVCF with zonula occludens (ZO)-1 and ZO-2: binding to PDZ-domain proteins and cell-cell adhesion regulate plasma membrane and nuclear localization of ARVCF. Mol. Biol. Cell 15, 5503–5515.

    PubMed  CAS  Google Scholar 

  • Kavanagh, E., Buchert, M., Tsapara, A., Choquet, A., Balda, M. S., Hollande, F., and Matter, K. (2006) Functional interaction between the ZO-1-interacting transcription factor ZONAB/DbpA and the RNA processing factor symplekin. J. Cell Sci. 119, 5098–5105.

    PubMed  CAS  Google Scholar 

  • Kelleher, R. J., 3rd, Govindarajan, A., Jung, H. Y., Kang, H., and Tonegawa, S. (2004) Trans lational control by MAPK signaling in long-term synaptic plasticity and memory. Cell 116, 467–479.

    PubMed  CAS  Google Scholar 

  • Kelly, K. F., Spring, C. M., Otchere, A. A., and Daniel, J. M. (2004) NLS-dependent nuclear localization of p120ctn is necessary to relieve Kaiso-mediated transcriptional repression. J. Cell Sci. 117, 2675–2686.

    PubMed  CAS  Google Scholar 

  • Kennedy, M. B. (1993) The postsynaptic density. Curr Opin Neurobiol 3, 732–737.

    PubMed  CAS  Google Scholar 

  • Kohu, K., Ogawa, F., and Akiyama, T. (2002) The SH3, HOOK and guanylate kinase-like domains of hDLG are important for its cytoplasmic localization. Genes Cells 7, 707–715.

    PubMed  CAS  Google Scholar 

  • Kress, T. L., Yoon, Y. J., and Mowry, K. L. (2004) Nuclear RNP complex assembly initiates cytoplasmic RNA localization. J. Cell Biol. 165, 203–211.

    PubMed  CAS  Google Scholar 

  • Lafarga, M., Andres, M. A., Fernandez-Viadero, C., Villegas, J., and Berciano, M. T. (1995) Number of nucleoli and coiled bodies and distribution of fibrillar centres in differentiating Purkinje neurons of chick and rat cerebellum. Anat. Embryol. (Berl) 191, 359–367.

    CAS  Google Scholar 

  • Laggerbauer, B., Ostareck, D., Keidel, E. M., Ostareck-Lederer, A., and Fischer, U. (2001) Evidence that fragile X mental retardation protein is a negative regulator of translation. Hum. Mol. Genet. 329–338.

    Google Scholar 

  • Lallena, M. J., Martinez, C., Valcarcel, J., and Correas, I. (1998) Functional association of nuclear protein 4.1 with pre-mRNA splicing factors. J. Cell Sci. 111 (Pt 14), 1963–1971.

    PubMed  CAS  Google Scholar 

  • Lewis, B. P., Green, R. E., and Brenner, S. E. (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. USA 100, 189–192.

    PubMed  CAS  Google Scholar 

  • Li, K., Hornshaw, M. P., van Minnen, J., Smalla, K. H., Gundelfinger, E. D., and Smit, A. B. (2005) Organelle proteomics of rat synaptic proteins: correlation-profiling by isotope- coded affinity tagging in conjunction with liquid chromatography-tandem mass spectrometry to reveal post-synaptic density specific proteins. J. Proteome Res. 4, 725–733.

    PubMed  CAS  Google Scholar 

  • Li, K. W., Hornshaw, M. P., Van Der Schors, R. C., Watson, R., Tate, S., Casetta, B., Jimenez, C. R., Gouwenberg, Y., Gundelfinger, E. D., Smalla, K. H., and Smit, A. B. (2004) Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology. J. Biol. Chem. 279, 987–1002.

    CAS  Google Scholar 

  • Li, Y., Yu, W. H., Ren, J., Chen, W., Huang, L., Kharbanda, S., Loda, M., and Kufe, D. (2003) Heregulin targets gamma-catenin to the nucleolus by a mechanism dependent on the DF3/MUC1 oncoprotein. Mol. Cancer Res. 1, 765–775.

    PubMed  CAS  Google Scholar 

  • Li, Z., Zhang, Y., Ku, L., Wilkinson, K. D., Warren, S. T., and Feng, Y. (2001) The fragile X mental retardation protein inhibits translation via interacting with mRNA. Nucleic Acids Res. 29, 2276–2283.

    PubMed  CAS  Google Scholar 

  • Lipscombe, D., Madison, D. V., Poenie, M., Reuter, H., Tsien, R. W., and Tsien, R. Y. (1988) Imaging of cytosolic Ca2+ transients arising from Ca2+ stores and Ca2+ channels in sympathetic neurons. Neuron 1, 355–365.

    PubMed  CAS  Google Scholar 

  • Liu, Y. Z., Dawson, S. J., and Latchman, D. S. (1996) Alternative splicing of the Brn-3a and Brn-3b transcription factor RNAs is regulated in neuronal cells. J. Mol. Neurosci. 7, 77- 85.

    PubMed  CAS  Google Scholar 

  • Macchi, P., Brownawell, A. M., Grunewald, B., DesGroseillers, L., Macara, I. G., and Kiebler, M. A. (2004) The brain-specific double-stranded RNA-binding protein Staufen2: nucleolar accumulation and isoform-specific exportin-5-dependent export. J. Biol. Chem. 279, 31440–31444.

    PubMed  CAS  Google Scholar 

  • Marambaud, P., Wen, P. H., Dutt, A., Shioi, J., Takashima, A., Siman, R., and Robakis, N. K. (2003) A CBP binding transcriptional repressor produced by the PS1/epsilon-cleavage of N-cadherin is inhibited by PS1 FAD mutations. Cell 114, 635–645.

    PubMed  CAS  Google Scholar 

  • Martel, C., Macchi, P., Furic, L., Kiebler, M. A., and Desgroseillers, L. (2006) Staufen1 is imported into the nucleolus via a bipartite nuclear localization signal and several modulatory determinants. Biochem. J. 393, 245–254.

    PubMed  CAS  Google Scholar 

  • Matsuda, S., Mikawa, S., and Hirai, H. (1999) Phosphorylation of serine-880 in GluR2 by protein kinase C prevents its C terminus from binding with glutamate receptor-interacting protein. J. Neurochem. 73, 1765–1768.

    PubMed  CAS  Google Scholar 

  • Mayeda, A., and Krainer, A. R. (1992) Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell 68, 365–375.

    PubMed  CAS  Google Scholar 

  • McGaugh, J. L. (2000) Memory–a century of consolidation. Science 287, 248–251.

    PubMed  CAS  Google Scholar 

  • Meissner, M., Lopato, S., Gotzmann, J., Sauermann, G., and Barta, A. (2003) Proto- oncoprotein TLS/FUS is associated to the nuclear matrix and complexed with splicing factors PTB, SRm160, and SR proteins. Exp. Cell Res. 283, 184–195.

    PubMed  CAS  Google Scholar 

  • Mu, Y., Otsuka, T., Horton, A. C., Scott, D. B., and Ehlers, M. D. (2003) Activity-dependent mRNA splicing controls ER export and synaptic delivery of NMDA receptors. Neuron 40, 581–594.

    PubMed  CAS  Google Scholar 

  • Murase, S., Mosser, E., and Schuman, E. M. (2002) Depolarization drives beta-Catenin into neuronal spines promoting changes in synaptic structure and function. Neuron 35, 91–105.

    PubMed  CAS  Google Scholar 

  • Nair, R., Carter, P., and Rost, B. (2003) NLSdb: database of nuclear localization signals. Nucleic Acids Res 31, 397–399.

    PubMed  CAS  Google Scholar 

  • Nakata, A., Ito, T., Nagata, M., Hori, S., and Sekimizu, K. (2004) GRIP1tau, a novel PDZ domain-containing transcriptional activator, cooperates with the testis-specific transcription elongation factor SII-T1. Genes Cells 9, 1125–1135.

    PubMed  CAS  Google Scholar 

  • Nimchinsky, E. A., Oberlander, A. M., and Svoboda, K. (2001) Abnormal development of dendritic spines in FMR1 knock-out mice. J. Neurosci. 21, 5139–5146.

    PubMed  CAS  Google Scholar 

  • Osawa, M., Tong, K. I., Lilliehook, C., Wasco, W., Buxbaum, J. D., Cheng, H. Y., Penninger, J. M., Ikura, M., and Ames, J. B. (2001) Calcium-regulated DNA binding and oligomerization of the neuronal calcium-sensing protein, calsenilin/DREAM/KChIP3. J. Biol. Chem. 276, 41005–41013.

    PubMed  CAS  Google Scholar 

  • Pastalkova, E., Serrano, P., Pinkhasova, D., Wallace, E., Fenton, A. A., and Sacktor, T. C. (2006) Storage of spatial information by the maintenance mechanism of LTP. Science 313, 1141–1144.

    PubMed  CAS  Google Scholar 

  • Patton, J. G., Porro, E. B., Galceran, J., Tempst, P., and Nadal-Ginard, B. (1993) Cloning and characterization of PSF, a novel pre-mRNA splicing factor. Genes Dev. 7, 393–406.

    PubMed  CAS  Google Scholar 

  • Peng, J., Kim, M. J., Cheng, D., Duong, D. M., Gygi, S. P., and Sheng, M. (2004) Semi-quantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spec trometry. J. Biol. Chem. 14, 21003–21011.

    Google Scholar 

  • Pfeiffer, B. E., and Huber, K. M. (2006) Current advances in local protein synthesis and synaptic plasticity. J. Neurosci. 26, 7147–7150.

    PubMed  CAS  Google Scholar 

  • Phillips, G. R., Florens, L., Tanaka, H., Khaing, Z. Z., Fidler, L., Yates, J. R., 3rd, and Colman, D. R. (2005) Proteomic comparison of two fractions derived from the transsynaptic scaffold. J. Neurosci. Res 81, 762–775.

    PubMed  CAS  Google Scholar 

  • Pinol-Roma, S., and Dreyfuss, G. (1992) Shuttling of pre-mRNA binding proteins between nucleus and cytoplasm. Nature 355, 730–732.

    PubMed  CAS  Google Scholar 

  • Polesello, C., and Payre, F. (2004) Small is beautiful: what flies tell us about ERM protein function in development. Trends Cell Biol. 14, 294–302.

    PubMed  CAS  Google Scholar 

  • Prieto, J. L., and McStay, B. (2005) Nucleolar biogenesis: the first small steps. Biochem. Soc. Trans. 33, 1441–1443.

    PubMed  CAS  Google Scholar 

  • Rajan, P., Symes, A. J., and Fink, J. S. (1996) STAT proteins are activated by ciliary neurotrophic factor in cells of central nervous system origin. J. Neurosci. Res 43, 403–411.

    PubMed  CAS  Google Scholar 

  • Ranum, L. P., and Cooper, T. A. (2006) RNA-mediated neuromuscular disorders. Annu. Rev. Neurosci. 29, 259–277.

    PubMed  CAS  Google Scholar 

  • Reymann, K. G., and Frey, J. U. (2007) The late maintenance of hippocampal LTP: Requirements, phases, ’synaptic tagging’, ’late-associativity’ and implications. Neuropharmacol. 52, 24–40.

    CAS  Google Scholar 

  • Righi, M., Tongiorgi, E., and Cattaneo, A. (2000) Brain-derived neurotrophic factor (BDNF) induces dendritic targeting of BDNF and tyrosine kinase B mRNAs in hippocampal neurons through a phosphatidylinositol-3 kinase-dependent pathway. J. Neurosci. 20, 3165–3174.

    PubMed  CAS  Google Scholar 

  • Roczniak-Ferguson, A., and Reynolds, A. B. (2003) Regulation of p120-catenin nucleocyto plasmic shuttling activity. J. Cell Sci. 116, 4201–4212.

    PubMed  CAS  Google Scholar 

  • Rodova, M., Kelly, K. F., VanSaun, M., Daniel, J. M., and Werle, M. J. (2004) Regulation of the rapsyn promoter by kaiso and delta-catenin. Mol. Cell Biol. 24, 7188–7196.

    PubMed  CAS  Google Scholar 

  • Rodriguez, M. A., Pesold, C., Liu, W. S., Kriho, V., Guidotti, A., Pappas, G. D., and Costa, E. (2000) Colocalization of integrin receptors and reelin in dendritic spine postsynaptic densities of adult nonhuman primate cortex. Proc. Natl. Acad. Sci. USA 97, 3550–3555.

    PubMed  CAS  Google Scholar 

  • Rook, M. S., Lu, M., and Kosik, K. S. (2000) CaMKIIalpha 3’ untranslated region-directed mRNA translocation in living neurons: visualization by GFP linkage. J. Neurosci. 20, 6385–6393.

    PubMed  CAS  Google Scholar 

  • Rothrock, C. R., House, A. E., and Lynch, K. W. (2005) HnRNP L represses exon splicing via a regulated exonic splicing silencer. EMBO J. 24, 2792–2802.

    PubMed  CAS  Google Scholar 

  • Salomon, D., Sacco, P. A., Roy, S. G., Simcha, I., Johnson, K. R., Wheelock, M. J., and Ben-Ze’ev, A. (1997) Regulation of beta-catenin levels and localization by overexpression of plakoglobin and inhibition of the ubiquitin-proteasome system. J. Cell Biol. 139, 1325–1335.

    PubMed  CAS  Google Scholar 

  • Santoni, V., Molloy, M., and Rabilloud, T. (2000) Membrane proteins and proteomics: unamour impossible? Electrophoresis 21, 1054–1070.

    PubMed  CAS  Google Scholar 

  • Scheiffele, P., Fan, J., Choih, J., Fetter, R., and Serafini, T. (2000) Neuroligin expressed in nonneuronal cells triggers presynaptic development in contacting axons. Cell 101, 657–669.

    PubMed  CAS  Google Scholar 

  • Schuman, E. M., Dynes, J. L., and Steward, O. (2006) Synaptic regulation of translation of dendritic mRNAs. J. Neurosci. 26, 7143–7146.

    PubMed  CAS  Google Scholar 

  • Shen, L., Liang, F., Walensky, L. D., and Huganir, R. L. (2000) Regulation of AMPA receptor GluR1 subunit surface expression by a 4. 1N-linked actin cytoskeletal association. J. Neurosci. 20, 7932–7940.

    PubMed  CAS  Google Scholar 

  • Shin, C., and Manley, J. L. (2004) Cell signalling and the control of pre-mRNA splicing. Nat Rev Mol Cell Biol 5, 727–738.

    PubMed  CAS  Google Scholar 

  • Si, K., Giustetto, M., Etkin, A., Hsu, R., Janisiewicz, A. M., Miniaci, M. C., Kim, J. H., Zhu, H., and Kandel, E. R. (2003) A neuronal isoform of CPEB regulates local protein synthesis and stabilizes synapse-specific long-term facilitation in aplysia. Cell 115, 893–904.

    PubMed  CAS  Google Scholar 

  • Siman, R., and Noszek, J. C. (1988) Excitatory amino acids activate calpain I and induce structural protein breakdown in vivo. Neuron 1, 279–287.

    PubMed  CAS  Google Scholar 

  • Simcha, I., Geiger, B., Yehuda-Levenberg, S., Salomon, D., and Ben-Ze’ev, A. (1996) Suppression of tumorigenicity by plakoglobin: an augmenting effect of N-cadherin. J. Cell Biol. 133, 199–209.

    PubMed  CAS  Google Scholar 

  • Solovei, I., Grandi, N., Knoth, R., Volk, B., and Cremer, T. (2004) Positional changes of pericentromeric heterochromatin and nucleoli in postmitotic Purkinje cells during murine cerebellum development. Cytogenetic and Genome Research 105, 302–310.

    Google Scholar 

  • Sossin, W. S., and DesGroseillers, L. (2006) Intracellular trafficking of RNA in neurons. Traffic 7, 1581–1589.

    PubMed  CAS  Google Scholar 

  • Steward, O., and Falk, P. M. (1986) Protein-synthetic machinery at postsynaptic sites during synaptogenesis: a quantitative study of the association between polyribosomes and developing synapses. J. Neurosci. 6, 412–423.

    PubMed  CAS  Google Scholar 

  • Steward, O., and Levy, W. B. (1982) Preferential localization of polyribosomes under the base of dendritic spines in granule cells of the dentate gyrus. J. Neurosci. 2, 284–291.

    PubMed  CAS  Google Scholar 

  • Steward, O., and Worley, P. F. (2001a) A cellular mechanism for targeting newly synthesized mRNAs to synaptic sites on dendrites. Proc. Natl. Acad. Sci. USA 98, 7062–7068.

    CAS  Google Scholar 

  • Steward, O., and Worley, P. F. (2001b) Selective targeting of newly synthesized Arc mRNA to active synapses requires NMDA receptor activation. Neuron 30, 227–240.

    CAS  Google Scholar 

  • Tang, S. J., Meulemans, D., Vazquez, L., Colaco, N., and Schuman, E. (2001) A role for a rat homolog of staufen in the transport of RNA to neuronal dendrites. Neuron 32, 463–475.

    PubMed  CAS  Google Scholar 

  • Thomas, K. L., Laroche, S., Errington, M. L., Bliss, T. V., and Hunt, S. P. (1994) Spatial and temporal changes in signal transduction pathways during LTP. Neuron 13, 737–745.

    PubMed  CAS  Google Scholar 

  • Thompson, K. R., Otis, K. O., Chen, D. Y., Zhao, Y., O’Dell, T. J., and Martin, K. C. (2004) Synapse to nucleus signaling during long-term synaptic plasticity; a role for the classical active nuclear import pathway. Neuron 44, 997–1009.

    PubMed  CAS  Google Scholar 

  • Tongiorgi, E., Righi, M., and Cattaneo, A. (1997) Activity-dependent dendritic targeting of BDNF and TrkB mRNAs in hippocampal neurons. J. Neurosci. 17, 9492–9505.

    PubMed  CAS  Google Scholar 

  • Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J. S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M., et al. (2005) Nova regulates brain-specific splicing to shape the synapse. Nat. Genet. 37, 844–852.

    PubMed  CAS  Google Scholar 

  • Usacheva, A., Smith, R., Minshall, R., Baida, G., Seng, S., Croze, E., and Colamonici, O. (2001) The WD motif-containing protein receptor for activated protein kinase C (RACK1) is required for recruitment and activation of signal transducer and activator of transcription 1 through the type I interferon receptor. J. Biol. Chem. 276, 22948–22953.

    PubMed  CAS  Google Scholar 

  • Vinade, L., Chang, M., Schlief, M. L., Petersen, J. D., Reese, T. S., Tao-Cheng, J. H., and Dosemeci, A. (2003) Affinity purification of PSD-95-containing postsynaptic complexes. J. Neurochem. 87, 1255–1261.

    PubMed  CAS  Google Scholar 

  • Walikonis, R. S., Jensen, O. N., Mann, M., Provance, D. W., Jr, Mercer, J. A., and Kennedy, M. B. (2000) Identification of Proteins in the Postsynaptic Density Fraction by Mass Spectrometry. J. Neurosci. 20, 4069–4080.

    PubMed  CAS  Google Scholar 

  • Walsh, M. J., and Kuruc, N. (1992) The postsynaptic density: constituent and associated prot eins characterized by electrophoresis, immunoblotting, and peptide sequencing. J. Neuro chem. 59, 667–678.

    CAS  Google Scholar 

  • Wang, G. S., Hong, C. J., Yen, T. Y., Huang, H. Y., Ou, Y., Huang, T. N., Jung, W. G., Kuo, T. Y., Sheng, M., Wang, T. F., and Hsueh, Y. P. (2004) Transcriptional modification by a CASK-interacting nucleosome assembly protein. Neuron 42, 113–128.

    PubMed  CAS  Google Scholar 

  • West, A. E., Griffith, E. C., and Greenberg, M. E. (2002) Regulation of transcription factors by neuronal activity. Nat. Rev. Neurosci. 3, 921–931.

    PubMed  CAS  Google Scholar 

  • Williams, C. C., Allison, J. G., Vidal, G. A., Burow, M. E., Beckman, B. S., Marrero, L., and Jones, F. E. (2004) The ERBB4/HER4 receptor tyrosine kinase regulates gene expression by functioning as a STAT5A nuclear chaperone. J. Cell Biol. 167, 469–478.

    PubMed  CAS  Google Scholar 

  • Woods, A. J., Roberts, M. S., Choudhary, J., Barry, S. T., Mazaki, Y., Sabe, H., Morley, S. J., Critchley, D. R., and Norman, J. C. (2002) Paxillin associates with poly(A)-binding protein 1 at the dense endoplasmic reticulum and the leading edge of migrating cells. J. Biol. Chem. 277, 6428–6437.

    PubMed  CAS  Google Scholar 

  • Wu, L., Wells, D., Tay, J., Mendis, D., Abbott, M. A., Barnitt, A., Quinlan, E., Heynen, A., Fallon, J. R., and Richter, J. D. (1998) CPEB-mediated cytoplasmic polyadenylation and the regulation of experience-dependent translation of alpha-CaMKII mRNA at synapses. Neuron 21, 1129–1139.

    PubMed  CAS  Google Scholar 

  • Wyszynski, M., Lin, J., Rao, A., Nigh, E., Beggs, A. H., Craig, A. M., and Sheng, M. (1997) Competitive binding of alpha-actinin and calmodulin to the NMDA receptor. Nature 385, 439–442.

    PubMed  CAS  Google Scholar 

  • Xie, J., Jan, C., Stoilov, P., Park, J., and Black, D. L. (2005) A consensus CaMK IV-responsive RNA sequence mediates regulation of alternative exons in neurons. RNA 11, 1825–1834.

    PubMed  CAS  Google Scholar 

  • Xu, H., and Hebert, M. D. (2005) A novel EB-1/AIDA-1 isoform, AIDA-1c, interacts with the Cajal body protein coilin. BMC. Cell Biol. 6, 23.

    PubMed  Google Scholar 

  • Yoshimura, Y., Yamauchi, Y., Shinkawa, T., Taoka, M., Donai, H., Takahashi, N., Isobe, T., and Yamauchi, T. (2004) Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J. Neurochem. 88, 759–768.

    PubMed  CAS  Google Scholar 

  • Yu, G., Zerucha, T., Ekker, M., and Rubenstein, J. L. (2001) Evidence that GRIP, a PDZ-domain protein which is expressed in the embryonic forebrain, co-activates transcription with DLX homeodomain proteins. Brain Res. Dev. Brain Res. 130, 217–230.

    PubMed  CAS  Google Scholar 

  • Zatsepina, O., Baly, C., Chebrout, M., and Debey, P. (2003) The step-wise assembly of a functional nucleolus in preimplantation mouse embryos involves the cajal (coiled) body. Dev. Biol. 253, 66–83.

    PubMed  CAS  Google Scholar 

  • Ziff, E. B. (1997) Enlightening the postsynaptic density. Neuron 19, 1163–1174.

    PubMed  CAS  Google Scholar 

  • Zinszner, H., Sok, J., Immanuel, D., Yin, Y., and Ron, D. (1997) TLS (FUS) binds RNA in vivo and engages in nucleo-cytoplasmic shuttling. J. Cell Sci. 110, 1741–1750.

    PubMed  CAS  Google Scholar 

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Jordan, B.A., Ziff, E.B. (2008). To the Nucleus with Proteomics. In: Dudek, S.M. (eds) Transcriptional Regulation by Neuronal Activity. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-73609-9_2

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